|
| Status |
Public on Aug 21, 2017 |
| Title |
H3K27ac CHIP-seq in shNS Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2_H3K27ac CHIP-seq in shNS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver cancer cell line
tranduced with: shNS
chip antibody: Histone H3K27ac antibody (pAb)
chip antibody vendor: Active Motif
chip antibody cat. #: 39133
chip antibody lot #: 3184008
|
| Treatment protocol |
cells were transfected with shRNA targeting BRG1 in the presence of 8ug/mL polybrene, and grown in 2ug/mL puromycin and harvested 7 days after transduction.
|
| Growth protocol |
HepG2 cellls were purchased from ATCC and grown in DMEM + 10%FCS + penicillin and streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa DNA hyperpep kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
H3K27ac_shNS_2
|
| Data processing |
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 30 --extendReads 150 --normalizeUsingRPKM --centerReads
macs2 callpeak -q 0.01 -keep-dup all --nomodel --extsize 150 -g hs --broad
peaks were filtered against blacklist (ENCODE) using bedtools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million
Supplementary_files_format_and_content: peaks are annotated against gencode v24 for nearest gene
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse Raab |
| E-mail(s) |
jesse.r.raab@gmail.com
|
| Organization name |
University of North Carolina Chapel Hill
|
| Department |
Genetics
|
| Street address |
120 Mason Farm Rd
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE102559 |
Cooperative and Antagonistic effects on SWI/SNF occupancy following BRG1 loss [ChIP-seq] |
| GSE102561 |
Co-regulation of transcription by BRG1 and Brm, two mutually exclusive SWI/SNF ATPase subunits |
|
| Relations |
| BioSample |
SAMN07500123 |
| SRA |
SRX3089119 |
